[Bioc-devel] problems installing cran dependencies with BioC devel in mac
Dan Tenenbaum
dtenenba at fredhutch.org
Wed Nov 30 23:06:17 CET 2016
----- Original Message -----
> From: "Sean Davis" <seandavi at gmail.com>
> To: "Martin Morgan" <martin.morgan at roswellpark.org>
> Cc: "bioc-devel" <bioc-devel at r-project.org>
> Sent: Wednesday, November 30, 2016 1:20:58 PM
> Subject: Re: [Bioc-devel] problems installing cran dependencies with BioC devel in mac
>> On Nov 30, 2016, at 4:13 PM, Martin Morgan <martin.morgan at roswellpark.org>
>> wrote:
>>
>> On 11/30/2016 08:51 AM, Kasper Daniel Hansen wrote:
>>> Full transcript please; you're compiling from source.
>>
>> Excuse my ignorance about the Mac world but shouldn't these be available for
>> binary installation via the URL Andrea provided,
>>
>> https://cran.rstudio.com/bin/macosx/mavericks/contrib/3.4/
>> <https://cran.rstudio.com/bin/macosx/mavericks/contrib/3.4/>
>
> I am not sure if it is supposed to be, but this directory is empty.
>
Building binaries of packages for R-devel is not always CRAN's highest priority, but it could be worth asking about. Simon Urbanek is the Mac person at CRAN.
Dan
> Sean
>
>
>>
>> ?
>>
>> Martin
>>
>>>
>>> On Wed, Nov 30, 2016 at 8:24 AM, Rodriguez Martinez, Andrea <
>>> andrea.rodriguez-martinez13 at imperial.ac.uk> wrote:
>>>
>>>> Hi,
>>>>
>>>>
>>>> Thanks for your reply. Maybe I am doing something wrong, but I do get
>>>> errors, after I select the option install from source. See below:
>>>>
>>>>
>>>>> source("https://bioconductor.org/biocLite.R")
>>>>> biocLite("MWASTools")
>>>>
>>>>
>>>> The downloaded source packages are in
>>>> ‘/private/var/folders/z8/8jwlrtqx3270h05ncg1xwzs80000gn
>>>> /T/Rtmp79qF9E/downloaded_packages’
>>>> Warning messages:
>>>> 1: In install.packages(pkgs = doing, lib = lib, ...) :
>>>> installation of package ‘SparseM’ had non-zero exit status
>>>> 2: In install.packages(pkgs = doing, lib = lib, ...) :
>>>> installation of package ‘irlba’ had non-zero exit status
>>>> 3: In install.packages(pkgs = doing, lib = lib, ...) :
>>>> installation of package ‘minqa’ had non-zero exit status
>>>> 4: In install.packages(pkgs = doing, lib = lib, ...) :
>>>> installation of package ‘RcppEigen’ had non-zero exit status
>>>> 5: In install.packages(pkgs = doing, lib = lib, ...) :
>>>> installation of package ‘quantreg’ had non-zero exit status
>>>> 6: In install.packages(pkgs = doing, lib = lib, ...) :
>>>> installation of package ‘lme4’ had non-zero exit status
>>>> 7: In install.packages(pkgs = doing, lib = lib, ...) :
>>>> installation of package ‘pbkrtest’ had non-zero exit status
>>>> 8: In install.packages(pkgs = doing, lib = lib, ...) :
>>>> installation of package ‘car’ had non-zero exit status
>>>> 9: In install.packages(pkgs = doing, lib = lib, ...) :
>>>> installation of package ‘igraph’ had non-zero exit status
>>>> 10: In install.packages(update[instlib == l, "Package"], l, repos =
>>>> repos, :
>>>> installation of package ‘mgcv’ had non-zero exit status
>>>>
>>>>
>>>>> sessionInfo()
>>>> R Under development (unstable) (2016-10-26 r71594)
>>>> Platform: x86_64-apple-darwin13.4.0 (64-bit)
>>>> Running under: OS X El Capitan 10.11.6
>>>>
>>>> locale:
>>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>>>
>>>> attached base packages:
>>>> [1] stats graphics grDevices utils datasets methods base
>>>>
>>>> other attached packages:
>>>> [1] BiocInstaller_1.25.2
>>>>
>>>> loaded via a namespace (and not attached):
>>>> [1] tools_3.4.0
>>>>
>>>>
>>>>
>>>> Thanks very much in advance,
>>>>
>>>>
>>>> Best wishes,
>>>>
>>>>
>>>> Andrea
>>>>
>>>> ________________________________
>>>> From: Vincent Carey <stvjc at channing.harvard.edu>
>>>> Sent: 30 November 2016 12:39:12
>>>> To: Rodriguez Martinez, Andrea
>>>> Cc: bioc-devel at r-project.org
>>>> Subject: Re: [Bioc-devel] problems installing cran dependencies with BioC
>>>> devel in mac
>>>>
>>>> In fact there was a problem installing igraph from source, but that is
>>>> another issue. That can
>>>> be resolved using the precompiled binary at http://igraph.org/r/#downloads
>>>>
>>>>
>>>>> sessionInfo()
>>>>
>>>> R Under development (unstable) (2016-10-26 r71594)
>>>>
>>>> Platform: x86_64-apple-darwin13.4.0 (64-bit)
>>>>
>>>> Running under: OS X El Capitan 10.11.6
>>>>
>>>>
>>>> locale:
>>>>
>>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>>>
>>>>
>>>> attached base packages:
>>>>
>>>> [1] stats graphics grDevices utils datasets methods base
>>>>
>>>>
>>>> other attached packages:
>>>>
>>>> [1] BiocInstaller_1.25.2 MWASTools_0.99.10 rmarkdown_1.1
>>>>
>>>>
>>>> loaded via a namespace (and not attached):
>>>>
>>>> [1] Rcpp_0.12.8 XVector_0.15.0
>>>>
>>>> [3] GenomeInfoDb_1.11.6 nloptr_1.0.4
>>>>
>>>> [5] ppcor_1.1 plyr_1.8.4
>>>>
>>>> [7] zlibbioc_1.21.0 tools_3.4.0
>>>>
>>>> [9] boot_1.3-18 digest_0.6.10
>>>>
>>>> [11] lme4_1.1-12 evaluate_0.10
>>>>
>>>> [13] tibble_1.2 gtable_0.2.0
>>>>
>>>> [15] nlme_3.1-128 lattice_0.20-34
>>>>
>>>> [17] mgcv_1.8-16 Matrix_1.2-7.1
>>>>
>>>> [19] igraph_1.0.1 parallel_3.4.0
>>>>
>>>> [21] SparseM_1.74 gridExtra_2.2.1
>>>>
>>>> [23] stringr_1.1.0 IRanges_2.9.8
>>>>
>>>> [25] S4Vectors_0.13.2 MatrixModels_0.4-1
>>>>
>>>> [27] stats4_3.4.0 grid_3.4.0
>>>>
>>>> [29] nnet_7.3-12 Biobase_2.35.0
>>>>
>>>> [31] qvalue_2.7.0 minqa_1.2.4
>>>>
>>>> [33] ggplot2_2.2.0 reshape2_1.4.2
>>>>
>>>> [35] car_2.1-3 glm2_1.1.2
>>>>
>>>> [37] magrittr_1.5 GenomicRanges_1.27.12
>>>>
>>>> [39] scales_0.4.1 htmltools_0.3.5
>>>>
>>>> [41] MASS_7.3-45 splines_3.4.0
>>>>
>>>> [43] BiocGenerics_0.21.0 assertthat_0.1
>>>>
>>>> [45] pbkrtest_0.4-6 SummarizedExperiment_1.5.3
>>>>
>>>> [47] colorspace_1.3-1 quantreg_5.29
>>>>
>>>> [49] stringi_1.1.2 lazyeval_0.2.0
>>>>
>>>> [51] munsell_0.4.3
>>>>
>>>> On Wed, Nov 30, 2016 at 7:27 AM, Vincent Carey <stvjc at channing.harvard.edu
>>>> <mailto:stvjc at channing.harvard.edu>> wrote:
>>>> sessionInfo()? I just did biocLite("MWASTools") with a devel version of
>>>> R/BiocInstaller,
>>>> and it seems to work well.
>>>>
>>>> On Wed, Nov 30, 2016 at 6:04 AM, Rodriguez Martinez, Andrea <
>>>> andrea.rodriguez-martinez13 at imperial.ac.uk<mailto:andrea.
>>>> rodriguez-martinez13 at imperial.ac.uk>> wrote:
>>>> Hi,
>>>>
>>>>
>>>> I'm trying to install my MWASTools package (devel branch) in mac, and I
>>>> get a lot of errors regarding the installation of the dependencies from
>>>> CRAN because there are no files in the repository:
>>>>
>>>> https://cran.rstudio.com/bin/macosx/mavericks/contrib/3.4/
>>>>
>>>>
>>>> For windows, I dont have any problems with the installation because the
>>>> cran repository has the files:
>>>>
>>>> https://cran.rstudio.com/bin/windows/contrib/r-devel/
>>>>
>>>>
>>>> One solution, is to install the CRAN dependencies in advance using
>>>>
>>>>> install.packages(pkgs, contriburl = "https://cran.rstudio.com/bin/
>>>> macosx/mavericks/contrib/3.3/")
>>>>
>>>>
>>>> I wonder if there is another solution to do this directly from biocLite.
>>>>
>>>>
>>>> Thanks very much,
>>>>
>>>>
>>>> Andrea
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
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>>>>
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>>>>
>>>>
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